Search results for "Free Energy"
showing 10 items of 170 documents
Melting temperature prediction by thermoelastic instability: An ab initio modelling, for periclase (MgO)
2021
Abstract Melting temperature (TM) is a crucial physical property of solids and plays an important role for the characterization of materials, allowing us to understand their behavior at non-ambient conditions. The present investigation aims i) to provide a physically sound basis to the estimation of TM through a “critical temperature” (TC), which signals the onset of thermodynamic instability due to a change of the isothermal bulk modulus from positive to negative at a given PC-VC-TC point, such that (∂P/∂V)VC,TC = -(∂2F/∂V2) VC,TC = 0; ii) to discuss the case of periclase (MgO), for which accurate melting temperature observations as a function of pressure are available. Using first princip…
Interferences in Locally Resonant Sonic Metamaterials Formed from Helmholtz Resonators
2019
[EN] The emergence of materials artificially designed to control the transmission of waves, generally called metamaterials, has been a hot topic in the field of acoustics for several years. The design of these metamaterials is usually carried out by overlapping different wave control mechanisms. An example of this trend is the so-called Locally Resonant Sonic Materials, being one of them the Phononic Crystals with a local resonant structure. These metamaterials are formed by sets of isolated resonators in such a way that the control of the waves is carried out by resonances and by the existence of Bragg bandgaps, which appear due to the ordered distribution of the resonators. Their use is b…
Quasi-RRHO approximation and DFT study for understanding the mechanism and kinetics of nitration reaction of benzonitrile with nitronium ion
2021
Abstract The nitration reaction of benzonitrile with nitronium cation, NO2+, has been studied within the Molecular Electron Density Theory at the MN15-L/aug-cc-pVTZ level of theory. For this electrophilic aromatic substitution (EAS) reaction, three regioisomeric reaction paths have been studied. Quasi-RRHO approximation was applied to consider the vibrational contribution to entropy and correct the Gibbs free energy profile of the reaction in the solvent phase. Benzonitrile is less nucleophilically activated than benzene due to the presence of the electron-withdrawing CN group the meta position is the more favorable reaction path of this EAS reaction. The analysis of ELF and AIM demonstrate…
Enhancing the sound absorption of small-scale 3D printed acoustic metamaterials based on Helmholtz resonators
2018
Acoustic metamaterials have recently become of interest for their ability to attenuate sound by breaking the mass-density law. In this paper, acoustic metamaterials based on Helmholtz resonators and capable of attenuating sound up to 30 dB are fabricated for sound absorption applications in the small scale. The proposed metamaterials are subwavelength at a factor of $\lambda /12$ with respect to the lateral dimension of the units. The directional response due to the position of the acoustic source on the sound attenuation provided by the metamaterial is investigated by controlling the location of a loudspeaker with a robot arm. To enhance and broaden the absorption bands, structural modific…
Stability of a Split Streptomycin Binding Aptamer
2016
Here we investigated the stability of an aptamer, which is formed by two RNA strands and binds the antibiotic streptomycin. Molecular dynamics simulations in aqueous solution confirmed the geometry and the pattern of hydrogen bond interactions that was derived from the crystal structure (1NTB). The result of umbrella sampling simulations indicated a favored streptomycin binding with a free energy of ΔGbind° = −101.7 kJ mol–1. Experimentally, the increase in oligonucleotide stability upon binding of streptomycin was probed by single-molecule force spectroscopy. Rate dependent force spectroscopy measurements revealed a decrease in the natural off-rate (koff-COMPLEX = 0.22 ± 0.16 s–1) for the …
The Active Inference Approach to Ecological Perception: General Information Dynamics for Natural and Artificial Embodied Cognition
2018
The emerging neurocomputational vision of humans as embodied, ecologically embedded, social agents – who shape and are shaped by their environment – offers a golden opportunity to revisit and revise ideas about the physical and information-theoretic underpinnings of life, mind, and consciousness itself. In particular, the active inference framework (AIF) makes it possible to bridge connections from computational neuroscience and robotics/AI to ecological psychology and phenomenology, revealing common underpinnings and overcoming key limitations. AIF opposes the mechanistic to the reductive, while staying fully grounded in a naturalistic and information theoretic foundation, using the princi…
Molecular Mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a Twister Ribozyme
2017
Published as part of the special collection of articles derived from the 10th Congress on Electronic Structure: Principles and Applications (ESPA-2016). The catalytic activity of some classes of natural RNA, named as ribozymes, has been discovered just in the past decades. In this paper, the cleavage of the RNA phosphodiester backbone has been studied in aqueous solution and in a twister ribozyme from Oryza sativa. The free energy profiles associated with a baseline substrate-assisted mechanism for the reaction in the enzyme and in solution were computed by means of free energy perturbation methods within hybrid QM/MM potentials, describing the chemical system by the M06-2× functional and t…
Negatively Charged Gangliosides Promote Membrane Association of Amphipathic Neurotransmitters
2018
Lipophilic neurotransmitters (NTs) such as dopamine are chemical messengers enabling neurotransmission by adhering onto the extracellular surface of the post-synaptic membrane in a synapse, followed by binding to their receptors. Previous studies have shown that the strength of the NT-membrane association is dependent on the lipid composition of the membrane. Negatively charged lipids such as phosphatidylserine, phosphatidylglycerol, and phosphatidic acid have been indicated to promote NT-membrane binding, however these anionic lipids reside almost exclusively in the intracellular leaflet of the post-synaptic membrane instead of the extracellular leaflet facing the synaptic cleft. Meanwhile…
Entropic Interactions between Two Knots on a Semiflexible Polymer.
2017
Two knots on a string can either be separated or intertwined, and may even pass through each other. At the microscopic scale, such transitions may occur spontaneously, driven by thermal fluctuations, and can be associated with a topological free energy barrier. In this manuscript, we study the respective location of a trefoil ( 3 1 ) and a figure-eight ( 4 1 ) knot on a semiflexible polymer, which is parameterized to model dsDNA in physiological conditions. Two cases are considered: first, end monomers are grafted to two confining walls of varying distance. Free energy profiles and transition barriers are then compared to a subset of free chains, which contain exactly one 3 1 and one 4 1 kn…
Fractional hereditariness of lipid membranes: Instabilities and linearized evolution
2016
In this work lipid ordering phase changes arising in planar membrane bilayers is investigated both accounting for elas- ticity alone and for effective viscoelastic response of such assemblies. The mechanical response of such membranes is studied by minimizing the Gibbs free energy which penalizes perturbations of the changes of areal stretch and their gradients only [1]. As material instabilities arise whenever areal stretches characterizing homogeneous configurations lie inside the spinoidal zone of the free energy density, bifurcations from such configurations are shown to occur as oscillatory perturbations of the in-plane displacement. Experimental observations [2] show a power-law in-pl…